9J6D | pdb_00009j6d

Structure of Chikungunya virus infectious particles, 2f block.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action.

Han, X.Ji, C.Tian, S.Wang, F.Cao, G.P.Li, D.Duan, X.Tong, Z.Qi, J.Wang, Q.Huang, Q.Zhan, B.D.Gao, G.F.Yan, J.

(2025) Nat Commun 16: 9682-9682

  • DOI: https://doi.org/10.1038/s41467-025-64687-2
  • Primary Citation of Related Structures:  
    9IW2, 9IXA, 9IXI, 9IYI, 9J6D

  • PubMed Abstract: 

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes febrile illness and acute or chronic arthritis. Most therapeutics are still in the pre-clinical stage. In this study, we report the isolation of two neutralizing antibodies, C34 and C37, from a convalescent patient and investigate their mechanisms of action. Both C34 and C37 exhibit high neutralizing activities in vitro and demonstrate protective effects against CHIKV in a female mouse model. Our functional and structural studies reveal a mechanism that inhibits multiple stages of the virus infection cycle. Both antibodies bind with high affinity to an epitope spanning E2, E1, and the connecting β-strands, facilitating intra- and inter-virion crosslinking. Cryo-EM structures additionally identify a minor patch located beneath the E3 binding site on E2, which is allosterically exposed upon E3 dissociation during virus maturation. Functional and structural data further suggest that binding to the CHIKV receptor, Mxra8, is obstructed due to a clash between the antibodies and the stalk region of Mxra8. Our results highlight the potential of antibody-based therapeutics against CHIKV and elucidate the mechanisms of monoclonal antibody protection.


  • Organizational Affiliation
    • CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
chikungunya E3A [auth U],
N [auth V],
O [auth W],
P [auth X]
55Chikungunya virusMutation(s): 0 
UniProt
Find proteins for A0A7S7YHM2 (Chikungunya virus)
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Go to UniProtKB:  A0A7S7YHM2
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UniProt GroupA0A7S7YHM2
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
chikungunya virus E1B [auth A],
C [auth B],
D [auth C],
E [auth D]
439Chikungunya virusMutation(s): 0 
Gene Names: CHIKVgp2
UniProt
Find proteins for A4L7I5 (Chikungunya virus)
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Go to UniProtKB:  A4L7I5
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UniProt GroupA4L7I5
Glycosylation
Glycosylation Sites: 1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
chikungunya E2F [auth E],
G [auth F],
H [auth G],
I [auth H]
414Chikungunya virusMutation(s): 0 
Gene Names: CHIKVgp2
UniProt
Find proteins for Q88628 (Chikungunya virus)
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Go to UniProtKB:  Q88628
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UniProt GroupQ88628
Glycosylation
Glycosylation Sites: 1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CHIKV capsid proteinJ [auth I],
K [auth J],
L [auth K],
M [auth L]
151Chikungunya virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for A0A6B9KBE1 (Chikungunya virus)
Explore A0A6B9KBE1 
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth M],
R [auth N],
S [auth O],
T [auth P]
4N-Glycosylation
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseU [auth Q],
V [auth R],
W [auth S],
X [auth T]
3N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.11 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China92369202

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release